|
jpayne@0
|
1 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10">
|
|
jpayne@0
|
2 <description>and associated distance metrics</description>
|
|
jpayne@0
|
3 <requirements>
|
|
jpayne@58
|
4 <container type="docker">quay.io/biocontainers/mulled-v2-d2e223d7ac457e81243657cd7ae8336bd1c16e8e:81b350b3fbf165cbf5db53022037a2657a660701-0</container>
|
|
jpayne@59
|
5 <!-- <requirement type="package" version="1.9">bcftools</requirement>
|
|
jpayne@58
|
6 <requirement type="package" version="1.0.8">bzip2</requirement>
|
|
jpayne@58
|
7 <requirement type="package" version="2.2.1">snp-pipeline</requirement>
|
|
jpayne@59
|
8 <requirement type="package" version="0.2.6">tabix</requirement> -->
|
|
jpayne@58
|
9 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
|
|
jpayne@0
|
10 </requirements>
|
|
jpayne@0
|
11 <command detect_errors="exit_code"><![CDATA[
|
|
jpayne@40
|
12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
|
|
jpayne@9
|
13 python $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
|
|
jpayne@0
|
14 #for $fa in sorted($cons, key=lambda f: f.element_identifier)
|
|
jpayne@0
|
15 -n $fa.element_identifier -f $fa
|
|
jpayne@0
|
16 #end for
|
|
jpayne@0
|
17 > ./file &&
|
|
jpayne@0
|
18 cat ./file &&
|
|
jpayne@0
|
19 cfsan_snp_pipeline snp_matrix -o $snpma ./file &&
|
|
jpayne@0
|
20 cfsan_snp_pipeline distance -p $pairws -m $distma $snpma &&
|
|
jpayne@0
|
21 cfsan_snp_pipeline snp_reference -l $snplist -o $referenceSNP $reference
|
|
jpayne@0
|
22 ]]></command>
|
|
jpayne@0
|
23 <inputs>
|
|
jpayne@0
|
24 <param type="data_collection" label="List of FASTA's" name="cons" format="fasta" collection_type="list" />
|
|
jpayne@0
|
25 <conditional name="reference">
|
|
jpayne@0
|
26 <param name="ref" type="select" label="Use a curated GalaxyTrakr reference, or a reference from your history" help="Choose whether to use one of our references or your own from your history">
|
|
jpayne@0
|
27 <option value="curated">Use a GalaxyTrakr reference</option>
|
|
jpayne@0
|
28 <option value="history">Use a reference from your history</option>
|
|
jpayne@0
|
29 </param>
|
|
jpayne@0
|
30 <when value="curated">
|
|
jpayne@0
|
31 <param name="reference" type="select" label="Select reference fasta">
|
|
jpayne@0
|
32 <options from_data_table="all_fasta">
|
|
jpayne@0
|
33 <filter type="sort_by" column="2"/>
|
|
jpayne@0
|
34 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
|
|
jpayne@0
|
35 </options>
|
|
jpayne@0
|
36 </param>
|
|
jpayne@0
|
37 </when>
|
|
jpayne@0
|
38 <when value="history">
|
|
jpayne@0
|
39 <param name="reference" type="data" format="fasta" label="Select reference fasta" />
|
|
jpayne@0
|
40 </when>
|
|
jpayne@0
|
41 </conditional>
|
|
jpayne@0
|
42 <param type="data" format="txt" name="snplist" label="SNP list from your history" />
|
|
jpayne@0
|
43 </inputs>
|
|
jpayne@0
|
44 <outputs>
|
|
jpayne@0
|
45 <data name="snpma" label="SNP matrix, fasta" format="fasta" />
|
|
jpayne@0
|
46 <data name="pairws" label="SNP pairwise matrix" format="tsv" />
|
|
jpayne@0
|
47 <data name="distma" label="SNP distance matrix" format="tsv" />
|
|
jpayne@38
|
48 <data name="referenceSNP" label="SNP Reference (FASTA)" format="fasta" />
|
|
jpayne@38
|
49 <data name="metrics" label="SNP matrix metrics" hidden="true" format="tsv" />
|
|
jpayne@0
|
50 </outputs>
|
|
jpayne@0
|
51 <tests>
|
|
jpayne@0
|
52 <test>
|
|
jpayne@0
|
53 <param name="cons">
|
|
jpayne@0
|
54 <collection type="list">
|
|
jpayne@0
|
55 <element name="sample1" value="samples/sample1/consensus.fasta" />
|
|
jpayne@0
|
56 <element name="sample2" value="samples/sample2/consensus.fasta" />
|
|
jpayne@0
|
57 <element name="sample3" value="samples/sample3/consensus.fasta" />
|
|
jpayne@0
|
58 <element name="sample4" value="samples/sample4/consensus.fasta" />
|
|
jpayne@0
|
59 </collection>
|
|
jpayne@0
|
60 </param>
|
|
jpayne@0
|
61 <param name="ref" value="history" />
|
|
jpayne@0
|
62 <param name="reference" value="reference/lambda_virus.fasta" />
|
|
jpayne@0
|
63 <param name="snplist" value="snplist.txt" />
|
|
jpayne@0
|
64 <output name="snpma" value="snpma.fasta" />
|
|
jpayne@0
|
65 <output name="pairws" value="snp_distance_pairwise.tsv" />
|
|
jpayne@0
|
66 <output name="distma" value="snp_distance_matrix.tsv" />
|
|
jpayne@0
|
67 <output name="referenceSNP" value="referenceSNP.fasta" />
|
|
jpayne@0
|
68 </test>
|
|
jpayne@0
|
69 </tests>
|
|
jpayne@0
|
70 <help><![CDATA[
|
|
jpayne@0
|
71 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
|
|
jpayne@0
|
72 ]]></help>
|
|
jpayne@0
|
73 <citations>
|
|
jpayne@0
|
74 <citation type="doi">10.7717/peerj-cs.20</citation>
|
|
jpayne@0
|
75 </citations>
|
|
jpayne@0
|
76 </tool> |
